#' Stacked Plots of Multichannel Sequences and/or Most Probable
#' Paths from Hidden Markov Models
#'
#' Function \code{ssplot} plots stacked sequence plots of sequence object
#' created with the \code{\link{seqdef}} function or observations and/or most
#' probable paths of \code{hmm} objects.
#'
#' @export
#'
#' @param x Either a hidden Markov model object of class \code{hmm} or a state
#'   sequence object of class \code{stslist} (created with the \code{\link[TraMineR]{seqdef}})
#'   function) or a list of state sequence objects.
#'
#' @param hidden.paths Output from \code{\link{hidden_paths}} function. Optional, if
#'   \code{x} is a \code{hmm} object or if \code{type = "obs"}.
#'
#' @param plots What to plot. One of \code{"obs"} for observations (the default),
#'   \code{"hidden.paths"} for most probable paths of hidden states,
#'   or \code{"both"} for observations and hidden paths together.
#'
#' @param type The type of the plot. Available types are \code{"I"} for sequence index
#'   plots and \code{"d"} for state distribution plots (the default). See
#'   \code{\link{seqplot}} for details.
#'
#' @param tlim Indexes of the subjects to be plotted (the default is 0,
#' i.e. all subjects are plotted). For example, \code{tlim = 1:10} plots
#' the first ten subjects in data.
#'
#' @param sortv A sorting variable or a sort method (one of \code{"from.start"},
#'   \code{"from.end"}, \code{"mds.obs"}, or \code{"mds.hidden"}) for
#'   \code{type = "I"}. The value \code{"mds.hidden"} is only available when
#'   hidden paths are available. Options \code{"mds.obs"} and
#'   \code{"mds.hidden"} automatically arrange the sequences according to the
#'   scores of multidimensional scaling (using \code{\link{cmdscale}}) for the
#'   observed data or hidden states paths.
#'   MDS scores are computed from distances/dissimilarities using a metric
#'   defined in argument \code{dist.method}. See \code{\link{plot.stslist}} for
#'   more details on \code{"from.start"} and \code{"from.end"}.
#'
#' @param sort.channel The number of the channel according to which the
#'   \code{"from.start"} or \code{"from.end"} sorting is done. Sorting according
#'   to hidden states is called with value 0. The default value is 1 (the first
#'   channel).
#'
#' @param dist.method The metric to be used for computing the distances of the
#'   sequences if multidimensional scaling is used for sorting. One of "OM"
#'   (optimal matching, the default), "LCP" (longest common prefix), "RLCP"
#'   (reversed LCP, i.e. longest common suffix), "LCS" (longest common
#'   subsequence), "HAM" (Hamming distance), and "DHD" (dynamic Hamming distance).
#'   Transition rates are used for defining substitution costs if needed. See
#'   \code{\link[TraMineR]{seqdef}} for more information on the metrics.
#'
#' @param with.missing Controls whether missing states are included in state
#'   distribution plots (\code{type = "d"}). The default is \code{FALSE}.
#'  
#' @param missing.color Alternative color for representing missing values 
#'   in the sequences. By default, this color is taken from the \code{missing.color} 
#'   attribute of the sequence object.
#'   
#' @param title Main title for the graphic. The default is \code{NA}: if
#'   \code{title.n = TRUE}, only the number of subjects is plotted. \code{FALSE}
#'   prints no title, even when \code{title.n = TRUE}.
#'
#' @param title.n Controls whether the number of subjects (in the
#'   first channel) is printed in the title of the plot. The default is
#'   \code{TRUE}: n is plotted if \code{title} is anything but \code{FALSE}.
#'
#' @param cex.title Expansion factor for setting the size of the font for the
#'   title. The default value is 1. Values lesser than 1 will reduce the size of
#'   the font, values greater than 1 will increase the size.
#'
#' @param title.pos Controls the position of the main title of the plot. The
#'   default value is 1. Values greater than 1 will place the title higher.
#'
#' @param with.legend Defines if and where the legend for the states is plotted.
#'   The default value \code{"auto"} (equivalent to \code{TRUE} and
#'   \code{"right"}) creates separate legends for each requested plot and
#'   positiones them on the right-hand side of the plot. Other possible values
#'   are \code{"bottom"},
#'   \code{"right.combined"}, and \code{"bottom.combined"}, of which the last
#'   two create a combined legend in the selected position. \code{FALSE} prints no legend.
#'
#' @param ncol.legend (A vector of) the number of columns for the legend(s). The
#'   default \code{"auto"} determines number of columns depending on the position of
#'   the legend.
#'
#' @param with.missing.legend If set to \code{"auto"} (the default), a legend
#'   for the missing state is added automatically if one or more of the
#'   sequences in the data/channel contains missing states and \code{type = "I"}.
#'   If \code{type = "d"} missing states are omitted from the legends unless
#'   \code{with.missing = TRUE}. With the value \code{TRUE} a
#'   legend for the missing state is added in any case; equivalently
#'   \code{FALSE} omits the legend for the missing state.
#'
#' @param legend.prop Sets the proportion of the graphic area used for plotting
#'   the legend when \code{with.legend} is not \code{FALSE}. The default value is
#'   0.3. Takes values from 0 to 1.
#'
#' @param cex.legend Expansion factor for setting the size of the font for the
#'   labels in the legend. The default value is 1. Values lesser than 1 will
#'   reduce the size of the font, values greater than 1 will increase the size.
#'
#' @param hidden.states.colors A vector of colors assigned to hidden states. The default
#'   value \code{"auto"} uses the colors assigned to the \code{stslist} object (created
#'   with \code{\link[TraMineR]{seqdef}}) if \code{hidden.paths} is given; otherwise colors from
#'   \code{\link{colorpalette}} are automatically used.
#'
#' @param hidden.states.labels Labels for the hidden states. The default value
#'   \code{"auto"} uses the names provided in \code{x$state_names} if \code{x} is
#'   an \code{hmm} object; otherwise the number of the hidden state.
#'
#' @param xaxis Controls whether an x-axis is plotted below the plot at the
#'   bottom. The default value is \code{TRUE}.
#'
#' @param xlab An optional label for the x-axis. If set to \code{NA}, no label
#'   is drawn.
#'
#' @param xtlab Optional labels for the x-axis tick labels.  If unspecified, the
#'   column names of the \code{seqdata} sequence object are used (see
#'   \code{\link[TraMineR]{seqdef}}).
#'
#' @param xlab.pos Controls the position of the x-axis label. The default value
#'   is 1. Values greater than 1 will place the label further away from the plot.
#'
#' @param ylab Labels for the channels shown as labels for y-axes.
#'   A vector of names for each channel
#'   (observations). The default value \code{"auto"} uses the names provided in
#'   \code{x$channel_names} if \code{x} is an \code{hmm} object; otherwise the
#'   names of the list in \code{x} if given, or the
#'   number of the channel if names are not given. \code{FALSE} prints no labels.
#'
#' @param hidden.states.title Optional label for the hidden state plot (in the
#'   y-axis). The default is \code{"Hidden states"}.
#'
#' @param yaxis Controls whether or not to plot the y-axis. The default is \code{FALSE}.
#'
#' @param ylab.pos Controls the position of the y axis labels (labels for
#'   channels and/or hidden states). Either \code{"auto"} or a numerical vector
#'   indicating how far away from the plots the titles are positioned. The
#'   default value \code{"auto"} positions all titles on line 1.
#'   Shorter vectors are recycled.
#'
#' @param cex.lab Expansion factor for setting the size of the font for the axis
#'   labels. The default value is 1. Values lesser than 1 will reduce the size
#'   of the font, values greater than 1 will increase the size.
#'
#' @param cex.axis Expansion factor for setting the size of the font for the x-axis
#'   tick labels. The default value is 1. Values lesser than 1 will reduce the size of
#'   the font, values greater than 1 will increase the size.
#' 
#' @param ... Other arguments to be passed on to
#'   \code{\link[TraMineR]{seqplot}}.
#'
#' @examples
#' data("biofam3c")
#'
#' # Creating sequence objects
#' child_seq <- seqdef(biofam3c$children, start = 15)
#' marr_seq <- seqdef(biofam3c$married, start = 15)
#' left_seq <- seqdef(biofam3c$left, start = 15)
#'
#' ## Choosing colors
#' attr(child_seq, "cpal") <- c("#66C2A5", "#FC8D62")
#' attr(marr_seq, "cpal") <- c("#AB82FF", "#E6AB02", "#E7298A")
#' attr(left_seq, "cpal") <- c("#A6CEE3", "#E31A1C")
#'
#'
#' # Plotting state distribution plots of observations
#' ssplot(list("Children" = child_seq, "Marriage" = marr_seq,
#' "Residence" = left_seq))
#'
#' \dontrun{
#' # Plotting sequence index plots of observations
#' ssplot(
#'   list(child_seq, marr_seq, left_seq), type = "I",
#'   # Sorting subjects according to the beginning of the 2nd channel (marr_seq)
#'   sortv = "from.start", sort.channel = 2,
#'   # Controlling the size, positions, and names for channel labels
#'   ylab.pos = c(1, 2, 1), cex.lab = 1, ylab = c("Children", "Married", "Residence"),
#'   # Plotting without legend
#'   with.legend = FALSE)
#'
#' # Plotting hidden Markov models
#'
#' # Loading a ready-made HMM for the biofam data
#' data("hmm_biofam")
#'
#' # Plotting observations and hidden states paths
#' ssplot(
#'   hmm_biofam, type = "I", plots = "both",
#'   # Sorting according to multidimensional scaling of hidden states paths
#'   sortv = "mds.hidden",
#'   ylab = c("Children", "Married", "Left home"),
#'   # Controlling title
#'   title = "Biofam", cex.title = 1.5,
#'   # Labels for x axis and tick marks
#'   xtlab = 15:30, xlab = "Age")
#'
#' # Computing the most probable paths of hidden states
#' hidden.paths <- hidden_paths(hmm_biofam)
#' hidden.paths_seq <- seqdef(hidden.paths, labels = paste("Hidden state", 1:5))
#'
#' # Plotting observations and hidden state paths
#' ssplot(
#'   hmm_biofam, type = "I", plots = "hidden.paths",
#'   # Sequence object of most probable paths
#'   hidden.paths = hidden.paths_seq,
#'   # Sorting according to the end of hidden state paths
#'   sortv = "from.end", sort.channel = 0,
#'   # Contolling legend position, type, and proportion
#'   with.legend = "bottom", legend.prop = 0.15,
#'   # Plotting without title and y label
#'   title = FALSE, ylab = FALSE)
#'   }
#' @seealso \code{\link{ssp}} for creating \code{ssp} objects and \code{\link{plot.ssp}}
#' and \code{\link{gridplot}} for plotting these;
#' \code{\link{build_hmm}} and \code{\link{fit_model}} for building and
#' fitting hidden Markov models; \code{\link{hidden_paths}} for
#' computing the most probable paths of hidden states; and \code{\link{biofam3c}}
#' \code{\link{hmm_biofam}} for information on the data and model used in the example.


ssplot <- function(x, hidden.paths = NULL,
                plots = "obs", type = "d", tlim = 0,
                sortv = NULL, sort.channel = 1, dist.method = "OM",
                with.missing = FALSE, missing.color = NULL,
                title = NA, title.n = TRUE, cex.title = 1, title.pos = 1,
                with.legend = "auto", ncol.legend = "auto",
                with.missing.legend = "auto",
                legend.prop = 0.3, cex.legend = 1,
                hidden.states.colors = "auto", hidden.states.labels = "auto",
                xaxis = TRUE, xlab = NA, xtlab = NULL, xlab.pos = 1,
                ylab = "auto", hidden.states.title = "Hidden states",
                yaxis = FALSE, ylab.pos = "auto",
                cex.lab = 1, cex.axis = 1, ...){
  
    check_deprecated_args(match.call())
  
  args <- as.list(match.call())[-1]
  args[[1]] <- eval(args[[1]], envir = parent.frame())
  sspargs <- do.call(ssp, args = args)
  plot.new()
  grid.newpage()
  savepar <- par(no.readonly = TRUE)
  on.exit(savepar, add = TRUE)
  do.call(SSPlotter, args = sspargs)
  par(savepar)
}
